/**
* General configuration
*/

if (!sessvars.karyoDas) {
	sessvars.karyoDas = new Object();
	sessvars.karyoDas.conf = new Object();
	sessvars.karyoDas.conf.sources = new Array();
	sessvars.karyoDas.conf.userEntryPoints = [3,5];
	sessvars.karyoDas.conf.zoomConf = [3,7498176,10788431];    
	sessvars.karyoDas.conf.userContainers = ['annotationListView', 'sequenceView', 'zoomView', 'bandView', 'chromosomeView','karyotypeView'];
	sessvars.karyoDas.conf.specie = new String();
	sessvars.karyoDas.conf.selectedDsnId = "Homo_sapiens.GRCh37.reference";
	/* DECIPHER PATIENT INFORMATION */
	sessvars.karyoDas.conf.decipher = new Object();
	sessvars.karyoDas.conf.decipher.patient = new Object();
	sessvars.karyoDas.conf.decipher.patient.source  = new Object();
	sessvars.karyoDas.conf.decipher.patient.source.annotations = new Array();
	
	sessvars.karyoDas.conf.decipher.patient.source.name = 'DECIPHER Patient 1876';
	  
	var eA = new Object();
	eA.id = 'del(3)(p25.3;p26.1){3.29 Mb}';
	eA.start = '7498176';
	eA.end = '10788431';
	eA.typeName = 'Patient annotation';
	eA.typeId = 'decipher:novel:ins:hard'; 
	eA.chromosomeId = 'chromosome3';
	eA.linkText = 'Decipher link';
	eA.linkUrl = 'https://decipher.sanger.ac.uk/application/patient/1876';
	sessvars.karyoDas.conf.decipher.patient.source.annotations.push(eA);
	  
	var eA = new Object();
	eA.id ='feature';
	eA.start = '1';
	eA.end = '10000000';
	eA.typeName = 'Patient annotation';
	eA.typeId = 'decipher:novel:ins:hard'; 
	eA.chromosomeId = 'chromosome5';
	eA.linkText = 'Decipher link';
	eA.linkUrl = 'url';
	sessvars.karyoDas.conf.decipher.patient.source.annotations.push(eA);
}

sessvars.karyoDas.conf.sources = new Array();
YAHOO.karyoDas.conf.selectedDsnId = "Homo_sapiens.GRCh37.reference";
//YAHOO.dasBrowser.genome.karyotypeStructure.dsn.selectedDsn.id = "Rattus_norvegicus.RGSC3.4.reference";
//YAHOO.dasBrowser.genome.karyotypeStructure.dsn.selectedDsn.id = "Canis_familiaris.BROADD2.reference";
//YAHOO.dasBrowser.genome.karyotypeStructure.karyotype.zoomConf.defaultValues = [1,153264619,154085448];
//YAHOO.karyoDas.conf.zoomConf = [];
//YAHOO.karyoDas.conf.userEntryPoints = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,'X','Y'];;
//YAHOO.karyoDas.conf.userContainers = ['annotationListView', 'sequenceView', 'zoomView', 'bandView', 'chromosomeView', 'karyotypeView']; //Possible containers ... ['annotationListView', 'sequenceView', 'zoomView', 'bandView', 'chromosomeView', 'karyotypeView', 'copyNumberView', 'test']
//YAHOO.karyoDas.conf.userContainers = [];

//DECIPHER
var source = new Object();
source.id = 'DS_223';
source.url ='http://das.sanger.ac.uk/das/decipher/features';
source.name ='DECIPHER';
source.label =['ENSEMBL'];
source.description ='Decipher IDs, positions, orientations and notes';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =null;
source.types = [];
source.stylesheet = true;
sessvars.karyoDas.conf.sources.push(source);

//ENSEMBL
var source = new Object();
source.id = 'local02';
source.url ='http://www.ensembl.org/das/Homo_sapiens.NCBI36.translation/features';
source.name ='Exon';
source.label =['ENSEMBL'];
source.description ='translation';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =1000000;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);


//HGNC
var source = new Object();
source.id = 'DS_700';
source.url ='http://das.sanger.ac.uk/das/hgnc36/features';
source.name ='HGNC mappings';
source.label =['ENSEMBL'];
source.description ='HGNC genes, mapped to NCBI36 chromosome coordinates.';
source.representation ='mark';
source.panel ='zoom';
source.ntLimit =17000000;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);

// NEW DGV
var source = new Object();
source.id = 'DS_702';
source.url ='http://das.ensembl.org/das/toronto_poly_36/features';
source.name ='Database of Genomic Variants';
source.label =['ENSEMBL'];
source.description ='Decipher:TorontoPoly';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =null;
source.types = [];
source.stylesheet = true;
sessvars.karyoDas.conf.sources.push(source);

//desmith
var source = new Object();
source.id = 'desmith';
source.url ='http://das.ensembl.org/das/desmith/features';
source.name ='deSmith';
source.label =['ENSEMBL'];
source.description ='deSmith';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =null;
source.types = [];
source.stylesheet = true;
sessvars.karyoDas.conf.sources.push(source);

//decipher_cnv_36
//var source = new Object();
//source.id = 'decipher_cnv_36';
//source.url ='http://das.sanger.ac.uk/das/decipher_cnv_36/features';
//source.name ='DECIPHER CNVs';
//source.label =['ENSEMBL'];
//source.description ='DECIPHER CNVs';
//source.representation ='track';
//source.panel ='chromosome';
//source.ntLimit =null;
//source.types = [];
//sessvars.karyoDas.conf.sources.push(source);


//WGTP regions
var source = new Object();
source.id = 'Redon Clones';
source.url ='http://das.sanger.ac.uk/das/WGTP_regions_36';
source.name ='Redon Clones';
source.label =['ENSEMBL'];
source.description ='Redon Clones';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =null;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);



//ens_36_omim_genes
var source = new Object();
source.id = 'ens_36_omim_genes';
source.url ='http://das.sanger.ac.uk/das/ens_36_omim_genes/features';
source.name ='Ensembl OMIM Genes';
source.label =['ENSEMBL'];
source.description ='Ensembl OMIM Genes';
source.representation ='track';
source.panel ='chromosome';
source.ntLimit =null;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);

//ens_36_imprinted_genes
var source = new Object();
source.id = 'Ensembl Imprinted Genes';
source.url ='http://das.sanger.ac.uk/das/ens_36_imprinted_genes/features';
source.name ='Ensembl Imprinted Genes';
source.label =['ENSEMBL'];
source.description ='Ensembl Imprinted Genes';
source.representation ='track';
source.panel ='chromosome';
source.ntLimit =null;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);

//intl_clonesets
var source = new Object();
source.id = 'intl_clonesets';
source.url ='http://das.sanger.ac.uk/das/intl_clonesets/features';
source.name ='International Clonesets';
source.label =['ENSEMBL'];
source.description ='International Clonesets';
source.representation ='track';
source.panel ='zoom';
source.ntLimit =17000000;
source.types = [];
sessvars.karyoDas.conf.sources.push(source);

//ucsf36
//var source = new Object();
//source.id = 'ucsf36';
//source.url ='http://das.sanger.ac.uk/das/ucsf36/features';
//source.name ='UCSF HumArray';
//source.label =['ENSEMBL'];
//source.description ='ucsf36';
//source.representation ='track';
//source.panel ='zoom';
//source.ntLimit =null;
//source.types = [];
//sessvars.karyoDas.conf.sources.push(source);

